obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

Cython API, taxonomy: fixed parental tree iterator (skipped second to

Browse Source 
last taxon, in OBI1 too)
This commit is contained in:
Celine Mercier
2019-03-26 14:08:54 +01:00
parent 06178d9d61
commit d8a7bd42bd
1 changed files with 4 additions and 4 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
python/obitools3/dms/taxo/taxo.pyx
View File

@ -113,7 +113,7 @@ cdef class Taxonomy(OBIWrapper) :
raise NotImplementedError() raise NotImplementedError()
cpdef Taxon get_taxon_by_taxid(self, int taxid): # TODO check deleted taxon behavior (403122) cpdef Taxon get_taxon_by_taxid(self, int taxid):
cdef ecotx_t* taxon_p cdef ecotx_t* taxon_p
cdef object taxon_capsule cdef object taxon_capsule
taxon_p = obi_taxo_get_taxon_with_taxid(self.pointer(), taxid) taxon_p = obi_taxo_get_taxon_with_taxid(self.pointer(), taxid)
@ -256,13 +256,13 @@ cdef class Taxonomy(OBIWrapper) :
cdef Taxon taxon cdef Taxon taxon
try: try:
taxon = self.get_taxon_by_taxid(taxid) taxon = self.get_taxon_by_taxid(taxid)
except: # TODO error handling (related to deleted taxon thing) except:
raise StopIteration raise StopIteration
if taxon is not None: if taxon is not None:
while taxon.parent.taxid != 1: # TODO was 0 before? while taxon.taxid != 1:
yield taxon yield taxon
taxon = taxon.parent taxon = taxon.parent
yield self[1] yield taxon
else: else:
raise StopIteration raise StopIteration